Heatmap

Number of Genes

Raf

Volcano Plot of Significant Genes

Volcano Plot of All Expressed Genes

Enrichments with EnrichR

Upregulated in Mutant

## Uploading data to Enrichr... Done.
##   Querying GO_Biological_Process_2018... Done.
##   Querying KEGG_2019... Done.
## Parsing results... Done.

Downregulated in Mutant

## Uploading data to Enrichr... Done.
##   Querying GO_Biological_Process_2018... Done.
##   Querying KEGG_2019... Done.
## Parsing results... Done.

GSEA Analysis

clusterProfiler

Using MSigDB C5

Pathway Visualisation

Toll Signalling Pathway

MAPK Signalling Pathway

Dorsal Target Genes

Dorsal Targets in the Mesoderm

Hypergeometric Test

q = nrow(zscores_meso)
m = nrow(zscores_meso)
n = nrow(counts(dds)) - nrow(zscores_meso)
k = nrow(ue)
  
phyper(q, m, n, k, lower.tail = FALSE)
## [1] 0

Dorsal Targets in the Neuroectoderm

Hypergeometric Test

q = nrow(zscores_neuroecto)
m = nrow(zscores_neuroecto)
n = nrow(counts(dds)) - nrow(ue)
k = nrow(ue)
  
phyper(q, m, n, k, lower.tail = FALSE)
## [1] 0

Dorsal Targets in the Ectoderm

Hypergeometric Test

q = nrow(zscores_ecto) - 1
m = nrow(zscores_ecto)
n = nrow(counts(dds)) - nrow(oe)
k = nrow(oe)
  
phyper(q, m, n, k, lower.tail = FALSE)
## [1] 4.851825e-05

Combined Heatmap

Session Info

## R version 4.0.5 (2021-03-31)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
##  [1] grid      parallel  stats4    stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] png_0.1-7                             VennDiagram_1.6.20                   
##  [3] futile.logger_1.4.3                   enrichR_3.0                          
##  [5] fgsea_1.16.0                          reactome.db_1.74.0                   
##  [7] pathview_1.30.1                       org.Dm.eg.db_3.12.0                  
##  [9] msigdbr_7.2.1                         ggrepel_0.9.1                        
## [11] cowplot_1.1.1                         ggpubr_0.4.0                         
## [13] data.table_1.14.0                     DT_0.17                              
## [15] forcats_0.5.1                         dplyr_1.0.5                          
## [17] purrr_0.3.4                           readr_1.4.0                          
## [19] tidyr_1.1.3                           tibble_3.1.0                         
## [21] ggplot2_3.3.3                         tidyverse_1.3.0                      
## [23] stringr_1.4.0                         enrichplot_1.13.0                    
## [25] ReactomePA_1.34.0                     clusterProfiler_3.18.1               
## [27] BSgenome.Dmelanogaster.UCSC.dm6_1.4.1 BSgenome_1.58.0                      
## [29] rtracklayer_1.50.0                    Biostrings_2.58.0                    
## [31] XVector_0.30.0                        pheatmap_1.0.12                      
## [33] geneplotter_1.68.0                    annotate_1.68.0                      
## [35] XML_3.99-0.6                          reshape_0.8.8                        
## [37] lattice_0.20-41                       gridExtra_2.3                        
## [39] RColorBrewer_1.1-2                    GenomicFeatures_1.42.3               
## [41] AnnotationDbi_1.52.0                  knitr_1.31                           
## [43] DESeq2_1.30.1                         SummarizedExperiment_1.20.0          
## [45] Biobase_2.50.0                        MatrixGenerics_1.2.1                 
## [47] matrixStats_0.58.0                    GenomicRanges_1.42.0                 
## [49] GenomeInfoDb_1.26.7                   IRanges_2.24.1                       
## [51] S4Vectors_0.28.1                      BiocGenerics_0.36.0                  
## 
## loaded via a namespace (and not attached):
##   [1] utf8_1.2.1               tidyselect_1.1.0         RSQLite_2.2.6           
##   [4] htmlwidgets_1.5.3        BiocParallel_1.24.1      scatterpie_0.1.5        
##   [7] munsell_0.5.0            withr_2.4.1              colorspace_2.0-0        
##  [10] GOSemSim_2.16.1          highr_0.8                rstudioapi_0.13         
##  [13] ggsignif_0.6.1           DOSE_3.16.0              labeling_0.4.2          
##  [16] KEGGgraph_1.50.0         GenomeInfoDbData_1.2.4   polyclip_1.10-0         
##  [19] bit64_4.0.5              farver_2.1.0             rprojroot_2.0.2         
##  [22] downloader_0.4           vctrs_0.3.7              treeio_1.14.4           
##  [25] generics_0.1.0           lambda.r_1.2.4           xfun_0.22               
##  [28] BiocFileCache_1.14.0     R6_2.5.0                 graphlayouts_0.7.1      
##  [31] locfit_1.5-9.4           bitops_1.0-6             cachem_1.0.4            
##  [34] DelayedArray_0.16.3      assertthat_0.2.1         scales_1.1.1            
##  [37] ggraph_2.0.5             gtable_0.3.0             tidygraph_1.2.0         
##  [40] rlang_0.4.10             genefilter_1.72.1        splines_4.0.5           
##  [43] rstatix_0.7.0            lazyeval_0.2.2           broom_0.7.6             
##  [46] checkmate_2.0.0          abind_1.4-5              BiocManager_1.30.12     
##  [49] yaml_2.2.1               reshape2_1.4.4           modelr_0.1.8            
##  [52] crosstalk_1.1.1          backports_1.2.1          qvalue_2.22.0           
##  [55] tools_4.0.5              ellipsis_0.3.1           jquerylib_0.1.3         
##  [58] Rcpp_1.0.6               plyr_1.8.6               progress_1.2.2          
##  [61] zlibbioc_1.36.0          RCurl_1.98-1.3           prettyunits_1.1.1       
##  [64] openssl_1.4.3            viridis_0.5.1            haven_2.3.1             
##  [67] fs_1.5.0                 magrittr_2.0.1           futile.options_1.0.1    
##  [70] openxlsx_4.2.3           DO.db_2.9                reprex_2.0.0            
##  [73] hms_1.0.0                patchwork_1.1.1          evaluate_0.14           
##  [76] xtable_1.8-4             rio_0.5.26               readxl_1.3.1            
##  [79] compiler_4.0.5           biomaRt_2.46.3           crayon_1.4.1            
##  [82] shadowtext_0.0.7         htmltools_0.5.1.1        aplot_0.0.6             
##  [85] lubridate_1.7.10         DBI_1.1.1                formatR_1.8             
##  [88] tweenr_1.0.2             dbplyr_2.1.1             MASS_7.3-53.1           
##  [91] rappdirs_0.3.3           Matrix_1.3-2             car_3.0-10              
##  [94] cli_2.4.0                igraph_1.2.6             pkgconfig_2.0.3         
##  [97] rvcheck_0.1.8            GenomicAlignments_1.26.0 foreign_0.8-81          
## [100] xml2_1.3.2               ggtree_2.4.2             bslib_0.2.4             
## [103] rvest_1.0.0              digest_0.6.27            graph_1.68.0            
## [106] rmarkdown_2.7            cellranger_1.1.0         fastmatch_1.1-0         
## [109] tidytree_0.3.4           curl_4.3                 Rsamtools_2.6.0         
## [112] graphite_1.36.0          rjson_0.2.20             lifecycle_1.0.0         
## [115] nlme_3.1-152             jsonlite_1.7.2           carData_3.0-4           
## [118] viridisLite_0.4.0        askpass_1.1              fansi_0.4.2             
## [121] pillar_1.6.0             KEGGREST_1.30.1          fastmap_1.1.0           
## [124] httr_1.4.2               survival_3.2-10          GO.db_3.12.1            
## [127] glue_1.4.2               zip_2.1.1                Rgraphviz_2.34.0        
## [130] bit_4.0.4                ggforce_0.3.3            stringi_1.5.3           
## [133] sass_0.3.1               blob_1.2.1               org.Hs.eg.db_3.12.0     
## [136] memoise_2.0.0            ape_5.5